For the FS format, definitively go for ext4. It shall save you a huge amount of time when fsck, it's easier to undelete from. For a media server usage you don't even need to understand the old delayed sync controversy, it's not relevant. For films, you're certainly right with Matroska. For the rest I wont comment (I use x264 myself).

Just shows once to your (young) nephew who is basically trustworthy how to get the very powerful magnet inside the drive. Switch nephew when he become tired to play with magnets. It worked for me for more than 30 drives so far.

Handbrake burns the subtitle into the film and doesn't allow to easily include several audio languages and subtitles. I'm multilingual and enjoy to see films with friends speaking various languages. The recent versions of OGMrip doesn't set the sound out of sync unless you jump back and forth inside the film.